docs: fixed CLI docs for tool commands
docs: fixed CLI docs for tool commands

ChrisTimperley/RepairBox,ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/RepairBox,ChrisTimperley/RepairBox,ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/RepairBox,ChrisTimperley/RepairBox,ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/RepairBox,ChrisTimperley/AutomatedRepairBenchmarks.c,squaresLab/RepairBox,ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/RepairBox,ChrisTimperley/RepairBox,ChrisTimperley/RepairBox,ChrisTimperley/RepairBox,ChrisTimperley/AutomatedRepairBenchmarks.c,ChrisTimperley/AutomatedRepairBenchmarks.c